User:Jeremy Chieh-Yu Chung/Sandbox 1

INTRODUCTION
Human beings fear when they hear the term “cancer.” When a person is diagnosed as having cancer, such news is always devastating. So, what is cancer? It is a disease in which cells exhibit uncontrolled growth and invasion that intrudes and kills adjacent tissue, and for most cases, it is lethal. Documents regarding to cancer can date as far back as 460BC, and reports on patients having symptoms resembling that of cancer could be found throughout the history of mankind. Ancient Greek physician Hippocrates described multiple kinds of cancers and referred them as carcinos. Since its discovery approximately 2500 years ago, there still is not a definite cure for the deadly disease. However, throughout the past few decades, with improved technology, medical communities now have a better understanding in treating the disease, or perhaps, slowing the spread of malignant cells. We now know that the onset of cancer is tightly related to the mutation in ras gene. Being involved in 30% of human cancer, hyperactive Ras is currently being heavily investigated as a possible target for novel drugs. Rat Sarcoma protein, also known as Ras, is the functional product of ras gene. It belongs to the large super-family of proteins known as “low-molecular weight G-proteins.” They are referred to as G-proteins due to their abilities to bind to guanine nucleotides (GTP and GDP). Ras is most commonly known by its ability to conduct extracellular signal to inside the cell. Ras triggers and causes responses in more than 20 effectors and regulate processes such as proliferation, survival and differentiation in cells.

HISTORY
When first investigated by scientists, two ras genes, HRAS and KRAS were identified as being responsible for the cancer-causing activities of sarcoma viruses. These viruses were found in rat, hence the name Rat sarcoma. Further investigations identified another ras gene in human neuroblastoma cells, the genes were designated as NRAS.

CLASSIFICATION
Ras protein is a member of small GTPases, and it is distinguished from the heterotrimeric G-proteins, often known as the large G protein. While both G protein subfamilies are capable of signal transduction and binding to GTP and GDP, the two differ in that heterotrimeric G proteins are made up of multiple subunits: alpha, beta and gamma, whereas small GTPases are monomeric. In fact, the small GTPases are homologous to the alpha subunit of the heterotrimers.

PDB ENTRY
3L8Z is classified as a oncoprotein with 166 residues. The structure was published in the May 2010 RCSB PDB [ ]

STRUCTURE
 Ras contains 5 alpha helices which are labeled in yellow and six-stranded beta sheets which are labeled in red. The G domain that binds to the guanosine nucleotide, has 166 amino acids with mass around 20kDa. It has five motifs that directly bind to either GDP or GTP. The five motifs are designated from G1 to G5 respectively. P-loops of G1 binds to the beta phosphate of GDP and GTP.Threonine-35 of G2, aspartate-57 of G3 , and alanine-146 of G5 all bind to GDP and GTP, while binding site for G4 is unclear. Binding of magnesium ions facilitate nucleotide binding to Ras. As Ras switches from its inactive to active state, two switches are moved. The first switch includes Threonine-35 of G2 and the second has a glycine-60 in DXXG motif.

ACTIVATION
Ras protein functions as a binary switch. When it is bound to GDP, the protein-GDP complex is in the resting, “off” state and when bound to GTP, which has an extra phosphate group compared to the GDP, it is in the active, “on” state. Only when G-protein is in its active state, can signals be transduced. The exchange between the two nucleotides is regulated by GAPs and GEFs. GAPs, also known as GTPase-activating proteins, allow Ras to return to its “off” state. On the other hand, GEFs, also known as guanine exchange factors return Ras to its active state. When under normal condition and triggered by growth factors, p21Ras proteins are involved in external stimuli transduction. Upon stimulation, Ras proteins become activated and transduce signals to effector molecules. Eventually the proteins become inactivated. However, mutated Ras proteins do not have the ability to become inactivated, thus stimulate cell differentiation and growth constantly even in the absence of stimuli.

MUTATION
Mutated Ras proteins are often characterized by both defects in intrinsic GTP hydrolysis and resistances to GAPs. Ras proteins with mutations that are constitutively active are permanently in their “active” state. Two of the most common locations for the mutations are residue glycine-12 found in the P loops and glutamine-61, which is a catalytic residue. Mutated Ras with change in amino acid from glycine to valine at residue 12 has a desensitized the GTPase domain of Ras. In another word, it would be more difficult for GAP to have an effect on mutated Ras. In the absence of GAP, the process of returning Ras from its active to inactive state would be very inefficient, thus, Ras would always be in its active state. Another mutation located at residue 61 that changes glutamine residue to lysine also results in permanently active Ras. The mutation drastically reduced the rate of intrinsic Ras GTP hydrolysis to the level that is almost unobservable. Indeed, inappropriate Ras signaling often leads to malignant cell transformation and proliferation. Indeed, Ras genes are the most common targets for somatic gain-of-function mutations in human cancer. Indeed, disorders such as Noonansyndrome, Costello syndrome and cardio-facio-cutaneous syndrome are found to have germ line mutations, which in turn affect the Ras-Raf-MEK-ERK pathways. FTIs, farnesyltransferase inhibitors are currently being administered to cancer patients in clinical trails. Preclinical data have supported selective antitumor effectors of these compounds. Indeed, FTIs have been shown to block Ras-induced transformation in tissue culture cells to inhibit the growth of many cancer cell lines and halt proliferation of Ras-activated mice.

FUNCTION
Ras proteins play crucial roles in human bodies. Recent studies have shown that nerve growth factor (NGF) has the capability of activating multiple downstream effectors with Ras being one of them. Sensory neurons having a small-diameter with heterozygous mutation of the tumor suppressor gene Nf1 gene exhibit increased excitability. In another word, Ras is less likely to be inactivated. Neurofibromin is not only the protein product of the Nf1 gene. The gene also encodes guanosine trophosphatase-activating protein (GAP) for p21ras. NGF enhances excitability of small-diameter sensory neurons in a Ras-dependent manner. Moreover, blocking Ras signaling cannot restore the consequence of decreased neurofibromin expression. This suggests that Ras-initiated signaling pathway can regulate both transcriptional and posttranslational control of ion channels important in neuronal excitability.

Another function of Ras can be observed when a person has a stroke. When experiencing cerebrovascular accident, he or she often suffered from selective neuronal cell death, which in turn causes damage in nervous system. Ras proteins’ abilities to integrate a wide range of intracellular signals make them crucial regulators and possible targets for neuronal recovery after stroke. Indeed, Ras family GTPases contributes greatly to neuroprotective signaling cascades.

As mentioned previously, p21ras serves as a binary switch in the activation of downstream effector pathways that governs the growth and differentiation of cells. The guanine nucleotide binding protein has an important role in the activation of T lymphocyte and positive selection of thymocyte. Such process is accomplished when the Ras protein couples the T cell antigen receptor (TCR) to the signaling pathways that regulate transcription factors important for the cytokine gene. Anergic T cells remain functionally inactive and do not initiate the appropriate immune response such as production of interleukin 2, IL-2, even in the presence of antigen. Studies have shown that T cell anergy is associated with defected GTPase Ras, which is correlated with diminished activation of mitogen-activated protein (MAP) kinase Erk, Ink, and other transcription factors. Experiments have shown that in anergic T cell, Ras proteins that are constitutively active are capable of restoring interleukin production, as well as MAP kinase activation.